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Zerbib E, Levin R, Gur E. Tag Recycling in the Pup-Proteasome System is Essential for Mycobacterium smegmatis Survival Under Starvation Conditions. Mol Microbiol 2024. [PMID: 39233599 DOI: 10.1111/mmi.15312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 07/28/2024] [Accepted: 08/14/2024] [Indexed: 09/06/2024]
Abstract
Many bacteria possess proteasomes and a tagging system that is functionally analogous to the ubiquitin system. In this system, Pup, the tagging protein, marks protein targets for proteasomal degradation. Despite the analogy to the ubiquitin system, where the ubiquitin tag is recycled, it remained unclear whether Pup is similarly recycled, given how the bacterial proteasome does not include a depupylase. We previously showed in vitro that as Pup lacks effective proteasome degradation sites, it is released from the proteasome following target degradation, remaining conjugated to a degradation fragment that can be later depupylated. Here, we tested this model in Mycobacterium smegmatis, using a Pup mutant that is effectively degraded by the proteasome. Our findings indicate that Pup recycling not only occurs in vivo but is also essential to maintain normal pupylome levels and to support bacterial survival under starvation conditions. Accordingly, Pup recycling is an essential process in the mycobacterial Pup-proteasome system.
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Affiliation(s)
- Erez Zerbib
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Roni Levin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
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2
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Janssen GV, Zhang S, Merkx R, Schiesswohl C, Chatterjee C, Darwin KH, Geurink PP, van der Heden van Noort GJ, Ovaa H. Development of Tyrphostin Analogues to Study Inhibition of the Mycobacterium tuberculosis Pup Proteasome System*. Chembiochem 2021; 22:3082-3089. [PMID: 34387015 PMCID: PMC8596589 DOI: 10.1002/cbic.202100333] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 08/12/2021] [Indexed: 11/29/2022]
Abstract
Tuberculosis is a global health problem caused by infection with the Mycobacterium tuberculosis (Mtb) bacteria. Although antibiotic treatment has dramatically reduced the impact of tuberculosis on the population, the existence and spreading of drug resistant strains urgently demands the development of new drugs that target Mtb in a different manner than currently used antibiotics. The prokaryotic ubiquitin-like protein (Pup) proteasome system is an attractive target for new drug development as it is unique to Mtb and related bacterial genera. Using a Pup-based fluorogenic substrate, we screened for inhibitors of Dop, the Mtb depupylating protease, and identified I-OMe-Tyrphostin AG538 (1) and Tyrphostin AG538 (2). The hits were validated and determined to be fast-reversible, non-ATP competitive inhibitors. We synthesized >25 analogs of 1 and 2 and show that several of the synthesized compounds also inhibit the depupylation actions of Dop on native substrate, FabD-Pup. Importantly, the pupylation activity of PafA, the sole Pup ligase in Mtb, was also inhibited by some of these compounds.
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Affiliation(s)
- Guido V. Janssen
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CenterEinthovenweg 202333 ZCLeidenThe Netherlands
- Division of Cell BiologyNetherlands Cancer InstitutePlesmanlaan 1211066 CXAmsterdamThe Netherlands
| | - Susan Zhang
- Department of MicrobiologyNew York University School of Medicine430 E. 29th StreetNew YorkNew York 10016USA
| | - Remco Merkx
- Division of Cell BiologyNetherlands Cancer InstitutePlesmanlaan 1211066 CXAmsterdamThe Netherlands
| | | | - Champak Chatterjee
- Department of ChemistryUniversity of WashingtonSeattleWashington 98195USA
| | - K. Heran Darwin
- Department of MicrobiologyNew York University School of Medicine430 E. 29th StreetNew YorkNew York 10016USA
| | - Paul P. Geurink
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CenterEinthovenweg 202333 ZCLeidenThe Netherlands
- Division of Cell BiologyNetherlands Cancer InstitutePlesmanlaan 1211066 CXAmsterdamThe Netherlands
| | - Gerbrand J. van der Heden van Noort
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CenterEinthovenweg 202333 ZCLeidenThe Netherlands
- Division of Cell BiologyNetherlands Cancer InstitutePlesmanlaan 1211066 CXAmsterdamThe Netherlands
| | - Huib Ovaa
- Oncode Institute and Department of Cell and Chemical BiologyLeiden University Medical CenterEinthovenweg 202333 ZCLeidenThe Netherlands
- Division of Cell BiologyNetherlands Cancer InstitutePlesmanlaan 1211066 CXAmsterdamThe Netherlands
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Zerbib E, Schlussel S, Hecht N, Bagdadi N, Eichler J, Gur E. The prokaryotic ubiquitin-like protein presents poor cleavage sites for proteasomal degradation. Cell Rep 2021; 36:109428. [PMID: 34320347 DOI: 10.1016/j.celrep.2021.109428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 05/09/2021] [Accepted: 06/30/2021] [Indexed: 11/17/2022] Open
Abstract
In an event reminiscent of eukaryotic ubiquitination, the bacterial prokaryotic ubiquitin-like protein (Pup)-proteasome system (PPS) marks target proteins for proteasomal degradation by covalently attaching Pup, the bacterial tagging molecule. Yet, ubiquitin is released from its conjugated target following proteasome binding, whereas Pup enters the proteasome and remains conjugated to the target. Here, we report that although Pup can be degraded by the bacterial proteasome, it lacks favorable 20S core particle (CP) cleavage sites and is thus a very poor 20S CP substrate. Reconstituting the PPS in vitro, we demonstrate that during pupylated protein degradation, Pup can escape unharmed and remain conjugated to a target-derived degradation fragment. Removal of this degradation fragment by Dop, a depupylase, facilitates Pup recycling and re-conjugation to a new target. This study thus offers a mechanistic model for Pup recycling and demonstrates how a lack of protein susceptibility to proteasome-mediated cleavage can play a mechanistic role in a biological system.
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Affiliation(s)
- Erez Zerbib
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Shai Schlussel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nir Hecht
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Noy Bagdadi
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Jerry Eichler
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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Izert MA, Klimecka MM, Górna MW. Applications of Bacterial Degrons and Degraders - Toward Targeted Protein Degradation in Bacteria. Front Mol Biosci 2021; 8:669762. [PMID: 34026843 PMCID: PMC8138137 DOI: 10.3389/fmolb.2021.669762] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/15/2021] [Indexed: 12/28/2022] Open
Abstract
A repertoire of proteolysis-targeting signals known as degrons is a necessary component of protein homeostasis in every living cell. In bacteria, degrons can be used in place of chemical genetics approaches to interrogate and control protein function. Here, we provide a comprehensive review of synthetic applications of degrons in targeted proteolysis in bacteria. We describe recent advances ranging from large screens employing tunable degradation systems and orthogonal degrons, to sophisticated tools and sensors for imaging. Based on the success of proteolysis-targeting chimeras as an emerging paradigm in cancer drug discovery, we discuss perspectives on using bacterial degraders for studying protein function and as novel antimicrobials.
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Affiliation(s)
| | | | - Maria Wiktoria Górna
- Structural Biology Group, Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Warsaw, Poland
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Korman M, Schlussel S, Vishkautzan M, Gur E. Multiple layers of regulation determine the cellular levels of the Pup ligase PafA inMycobacterium smegmatis. Mol Microbiol 2019; 112:620-631. [DOI: 10.1111/mmi.14278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Maayan Korman
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva 84105Israel
| | - Shai Schlussel
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva 84105Israel
| | - Marina Vishkautzan
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva 84105Israel
- The National Institute for Biotechnology in the Negev Ben‐Gurion University of the Negev Beer‐Sheva84105Israel
| | - Eyal Gur
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva 84105Israel
- The National Institute for Biotechnology in the Negev Ben‐Gurion University of the Negev Beer‐Sheva84105Israel
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Pupylated proteins are subject to broad proteasomal degradation specificity and differential depupylation. PLoS One 2019; 14:e0215439. [PMID: 31009487 PMCID: PMC6476560 DOI: 10.1371/journal.pone.0215439] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 04/02/2019] [Indexed: 11/19/2022] Open
Abstract
In actinobacteria, post-translational modification of proteins with prokaryotic ubiquitin-like protein Pup targets them for degradation by a bacterial proteasome assembly consisting of the 20S core particle (CP) and the mycobacterial proteasomal ATPase (Mpa). Modification of hundreds of cellular proteins with Pup at specific surface lysines is carried out by a single Pup-ligase (PafA, proteasome accessory factor A). Pupylated substrates are recruited to the degradative pathway by binding of Pup to the N-terminal coiled-coil domains of Mpa. Alternatively, pupylation can be reversed by the enzyme Dop (deamidase of Pup). Although pupylated substrates outcompete free Pup in proteasomal degradation, potential discrimination of the degradation complex between the various pupylated substrates has not been investigated. Here we show that Mpa binds stably to an open-gate variant of the proteasome (oCP) and associates with bona fide substrates with highly similar affinities. The proteasomal degradation of substrates differing in size, structure and assembly state was recorded in real-time, showing that the pupylated substrates are processed by the Mpa-oCP complex with comparable kinetic parameters. Furthermore, the members of a complex, pupylated proteome (pupylome) purified from Mycobacterium smegmatis are degraded evenly as followed by western blotting. In contrast, analysis of the depupylation behavior of several pupylome members suggests substrate-specific differences in enzymatic turnover, leading to the conclusion that largely indiscriminate degradation competes with differentiated depupylation to control the ultimate fate of pupylated substrates.
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Korman M, Elharar Y, Fishov I, Gur E. The transcription of pafA, encoding the prokaryotic ubiquitin-like protein ligase, is regulated by PafBC. Future Microbiol 2018; 14:11-21. [PMID: 30547686 DOI: 10.2217/fmb-2018-0278] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Mycobacterium tuberculosis possesses an intracellular tagging and degradation system, which has emerged as a target for development of anti-tuberculosis agents. In this system, PafA is the ligase that marks proteins for degradation by their covalent modification with a protein modifier. Here, we studied pafA transcriptional regulation, which remained elusive despite its importance for M. tuberculosis virulence. MATERIALS & METHODS Working with Mycobacterium smegmatis, a mycobacterial model organism, we examined the involvement of the global regulators PafB and PafC in pafA regulation. RESULTS PafBC activated pafA transcription following DNA damage, resulting in efficient cellular recovery. CONCLUSION The results unraveled the involvement of PafBC in pafA transcription, and revealed the importance of proper PafA regulation in mycobacterial physiology.
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Affiliation(s)
- Maayan Korman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yifat Elharar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Itzhak Fishov
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Petchiappan A, Chatterji D. Pup recycling regulates the proteasome. FEBS J 2017. [PMID: 28627115 DOI: 10.1111/febs.14112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Pup proteasome system (PPS) in bacteria is equivalent to the eukaryotic ubiquitin proteasome system (UPS) that allows controlled protein degradation. Unlike the UPS, however, the PPS machinery and regulation is still poorly understood. In this issue of The FEBS Journal, Gur and colleagues combine experimental and modelling analyses to show how the PPS maintains steady-state levels of protein pupylation and consequently tightly controlled protein degradation.
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Affiliation(s)
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Gur E, Korman M, Hecht N, Regev O, Schlussel S, Silberberg N, Elharar Y. How to control an intracellular proteolytic system: Coordinated regulatory switches in the mycobacterial Pup-proteasome system. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2253-2260. [PMID: 28887055 DOI: 10.1016/j.bbamcr.2017.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/26/2017] [Accepted: 08/31/2017] [Indexed: 10/18/2022]
Abstract
Intracellular proteolysis is critical for the proper functioning of all cells, owing to its involvement in a wide range of processes. Because of the destructive nature of protein degradation, intracellular proteolysis is restricted by control mechanisms at almost every step of the proteolytic process. Understanding the coordination of such mechanisms is a challenging task, especially in systems as complex as the eukaryotic ubiquitin-proteasome system (UPS). In comparison, the bacterial analog of the UPS, the Pup-proteasome system (PPS) is much simpler and, therefore, allows for insight into the control of a proteolytic system. This review integrates available information to present a coherent picture of what is known of PPS regulatory switches and describes how these switches act in concert to enforce regulation at the system level. Finally, open questions regarding PPS regulation are discussed, providing readers with a sense of what lies ahead in the field.
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Affiliation(s)
- Eyal Gur
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| | - Maayan Korman
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nir Hecht
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Ofir Regev
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Shai Schlussel
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Nimrod Silberberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; The National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Yifat Elharar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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Delley CL, Müller AU, Ziemski M, Weber-Ban E. Prokaryotic Ubiquitin-Like Protein and Its Ligase/Deligase Enyzmes. J Mol Biol 2017; 429:3486-3499. [PMID: 28478282 DOI: 10.1016/j.jmb.2017.04.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 04/11/2017] [Accepted: 04/28/2017] [Indexed: 11/30/2022]
Abstract
Prokaryotic ubiquitin-like protein (Pup) and the modification enzymes involved in attaching Pup to or removing it from target proteins present a fascinating example of convergent evolution with respect to eukaryotic ubiquitination. Like ubiquitin (Ub), Pup is a small protein that can be covalently attached to lysine side chains of cellular proteins, and like Ub, it can serve to recruit tagged proteins for proteasomal degradation. However, unlike Ub, Pup is conformationally highly dynamic, exhibits a different linkage connectivity to its target lysines, and its ligase belongs to a different class of enzymes than the E1/E2/E3 cascade of ubiquitination. A specific feature of actinobacteria (aside from sporadic cases in a few other lineages), pupylation appears to have evolved to provide an advantage to the bacteria under certain environmental stresses rather than act as a constitutive modification. For Mycobacterium tuberculosis, pupylation and the recruitment of pupylated substrates to the proteasome support persistence inside host macrophages during pathogenesis, rendering the Pup-proteasome system an attractive drug target. In this review, we consider the dynamic nature of Pup in relation to its function, discuss the reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, and put them in context of the evolutionary history of this post-translational modification.
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Affiliation(s)
- Cyrille L Delley
- ETH Zurich, Institute of Molecular Biology & Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Andreas U Müller
- ETH Zurich, Institute of Molecular Biology & Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Michal Ziemski
- ETH Zurich, Institute of Molecular Biology & Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Eilika Weber-Ban
- ETH Zurich, Institute of Molecular Biology & Biophysics, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
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